1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
|
import os
import unittest
from rdkit import Chem, RDConfig
from rdkit.Chem import rdConformerParser
from rdkit.RDLogger import logger
logger = logger()
class TestCase(unittest.TestCase):
def setUp(self):
pass
def testReadAmberTraj(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'test_data', 'water_coords.trx')
mol = Chem.MolFromSmiles('O')
mol = Chem.AddHs(mol)
ids = rdConformerParser.AddConformersFromAmberTrajectory(mol, fileN)
self.assertTrue(mol.GetNumConformers() == 1)
self.assertTrue(len(ids) == 1)
self.assertTrue(ids[0] == 0)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'test_data', 'water_coords2.trx')
ids = rdConformerParser.AddConformersFromAmberTrajectory(mol, fileN, clearConfs=True)
self.assertTrue(mol.GetNumConformers() == 2)
ids = rdConformerParser.AddConformersFromAmberTrajectory(mol, fileN, clearConfs=False)
self.assertTrue(mol.GetNumConformers() == 4)
ids = rdConformerParser.AddConformersFromAmberTrajectory(mol, fileN, numConfs=1,
clearConfs=True)
self.assertTrue(mol.GetNumConformers() == 1)
if __name__ == '__main__':
unittest.main()
|
